Usp39 ubiquitin specific peptidase 39 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Usp39provided by MGI
Official Full Name: ubiquitin specific peptidase 39provided by MGI
Primary source: MGI:MGI:107622
See related: Ensembl:ENSMUSG00000056305 AllianceGenome:MGI:107622
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: SAD1; CGI-21; D6Wsu157e
Summary: Predicted to enable cysteine-type deubiquitinase activity and zinc ion binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to be located in nucleoplasm. Predicted to be part of U4/U6 x U5 tri-snRNP complex. Is expressed in cerebral cortex; early conceptus; and genitourinary system. Orthologous to human USP39 (ubiquitin specific peptidase 39). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Ubiquitous expression in placenta adult (RPKM 20.2), liver E14 (RPKM 19.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 C1; 6 32.27 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (72295749..72322190, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (72318676..72345208, complement)

Chromosome 6 - NC_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy.
Title: Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy.
USP39 Regulates NF-kappaB-Mediated Inflammatory Responses through Deubiquitinating K48-Linked IkappaBalpha.
Title: USP39 Regulates NF-κB-Mediated Inflammatory Responses through Deubiquitinating K48-Linked IκBα.
High expression of ubiquitin-specific peptidase 39 is associated with the development of vascular remodeling.
Title: High expression of ubiquitin-specific peptidase 39 is associated with the development of vascular remodeling.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3) 1 citation
Targeted (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Usp39 (e-PCR), detects polymorphism
- UniSTS:532503

D6Wsu157e (e-PCR), detects polymorphism
- UniSTS:142650

RH124797 (e-PCR)
- UniSTS:161619

RH130860 (e-PCR)
- UniSTS:214144

AI894154 (e-PCR)
- UniSTS:179395

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables cysteine-type deubiquitinase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein deubiquitination	IEA Inferred from Electronic Annotation more info
involved_in spliceosomal complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosomal complex assembly	ISO Inferred from Sequence Orthology more info
involved_in spliceosomal complex assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of U4/U6 x U5 tri-snRNP complex	ISO Inferred from Sequence Orthology more info
part_of U4/U6 x U5 tri-snRNP complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase 39

Names: SnRNP assembly defective 1 homolog; U4/U6.U5 tri-snRNP-associated 65 kDa protein; U4/U6.U5 tri-snRNP-associated protein 2; inactive ubiquitin-specific peptidase 39; ubiquitin specific protease 39

NP_001397563.1

EC 3.4.19.12

NP_613058.1

EC 3.4.19.12

XP_006506279.1

EC 3.4.19.12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001410634.1 → NP_001397563.1 ubiquitin carboxyl-terminal hydrolase 39 isoform 2

Status: VALIDATED

Source sequence(s)

AC116115
NM_138592.5 → NP_613058.1 ubiquitin carboxyl-terminal hydrolase 39 isoform 1

Status: VALIDATED

Source sequence(s)

AC116115

Consensus CDS

CCDS20238.1

UniProtKB/Swiss-Prot

Q3TI55, Q3TIX9, Q8BLI5, Q8BZZ5, Q9CQR1

Related

ENSMUSP00000064515.4, ENSMUST00000070345.5

Conserved Domains (3) summary

cd02669
Location:105 → 552

Peptidase_C19M; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

pfam00443
Location:223 → 551

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam12300
Location:3 → 93

DUF3628; Protein of unknown function (DUF3628)

RNA

NR_177101.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC116115

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

72295749..72322190 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006506216.5 → XP_006506279.1 ubiquitin carboxyl-terminal hydrolase 39 isoform X2

Conserved Domains (2) summary

PRK04537
Location:3 → 93

PRK04537; ATP-dependent RNA helicase RhlB; Provisional

cd02669
Location:105 → 550

Peptidase_C19M; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...